6.2. Possible Conversion

Plot directed graph of possible conversion

from bioconvert.core.graph import create_graph

If you use pygraphviz, you can have a good quality image using:

import matplotlib as mpl

mpl.rcParams["figure.dpi"] = 250

In order to create the following image, you need graphviz and pygraphviz. If you cannot install those packages, you may use a singularity image like in the following example by setting the use_singularity parameter to True. This would work under Linux. Not tested on other systems yet.

try:
    create_graph("conversion.png", use_singularity=True)
except:
    create_graph("conversion.png", use_singularity=False)

Creating directory /home/docs/.config/bioconvert
Downloading singularity. Please wait
singularity pull --name /home/docs/.config/bioconvert/graphviz.simg  shub://cokelaer/graphviz4all:v1
Warning ! Singularity must be installed if you want to you used it ! Switching to local graphviz executable if available

from pylab import imshow, imread, xticks, yticks, gca

imshow(imread("conversion.png"), interpolation="nearest")
xticks([])
yticks([])
ax = gca()
ax.axis("off")

(-0.5, 2756.5, 634.5, -0.5)